[gmx-users] MDRUN crash
Mark Abraham
mark.j.abraham at gmail.com
Fri Jun 17 08:46:43 CEST 2016
Hi,
Please don't start new work with old out-of-maintenance software, or at
least use the most recent bug fix from that release branch. You should also
do an equilibration with a normal acetone first, so that you know whether
it's your equilibration or your shell model that is the problem.
Mark
On Fri, Jun 17, 2016 at 8:44 AM Luca Banetta <luca.banetta at gmail.com> wrote:
> thank you for the advice justin! i have made some research and i use PME
> for electrostatics that i noticed it's pretty common. Unfortunately the
> mdrun this fatal error appeared:
> Program mdrun, VERSION 4.5.4
> Source code file: pme.c, line: 538
>
> Fatal error:
> 1629 particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
>
> For out simulation we created a topology for the acetone molecule using
> opls-AA force field introudicing a shell particle inside the topology.
> At the moment the simulation is based on a single acetone molecule inside a
> "sea" of water.
> [ moleculetype ]
> ; Name nrexcl
> acetone 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge
> mass typeB chargeB massB
> 1 opls_280 1 LIG C 1 0.47
> 12.011
> 2 opls_135 1 LIG C 2 -0.18
> 12.011
> 3 opls_135 1 LIG C 3 -0.18
> 12.011
> 4 opls_281 1 LIG O 4 0.47
> 15.5994
> 5 opls_282 1 LIG H 5 0.06
> 1.008
> 6 opls_282 1 LIG H 6 0.06
> 1.008
> 7 opls_282 1 LIG H 7 0.06
> 1.008
> 8 opls_282 1 LIG H 8 0.06
> 1.008
> 9 opls_282 1 LIG H 9 0.06
> 1.008
> 10 opls_282 1 LIG H 10 0.06
> 1.008
> 11 VS 1 LIG VS 11
> -0.47 0.000
> 12 SP 1 LIG SP 12
> -0.47 0.000
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 4 11 6
> 11 12 6
> 2 5 1
> 2 6 1
> 2 7 1
> 3 8 1
> 3 9 1
> 3 10 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 2 8 1
> 2 9 1
> 2 10 1
> 3 5 1
> 3 6 1
> 3 7 1
> 4 5 1
> 4 6 1
> 4 7 1
> 4 8 1
> 4 9 1
> 4 10 1
>
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> 2 1 3 1
> 2 1 4 1
> 3 1 4 1
> 1 2 5 1
> 1 2 6 1
> 1 2 7 1
> 5 2 6 1
> 5 2 7 1
> 6 2 7 1
> 1 3 8 1
> 1 3 9 1
> 1 3 10 1
> 8 3 9 1
> 8 3 10 1
> 9 3 10 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 3 1 2 5 3
> 3 1 2 6 3
> 3 1 2 7 3
> 4 1 2 5 3
> 4 1 2 6 3
> 4 1 2 7 3
> 2 1 3 8 3
> 2 1 3 9 3
> 2 1 3 10 3
> 4 1 3 8 3
> 4 1 3 9 3
> 4 1 3 10 3
>
> [ virtual_sites2 ]
> ; site ai aj funct a
> 11 1 4 1 1.05
>
> VS and SP have been introduced in the "ffnonbonded" and "ffbonded" sections
> in the library oplsaa.ff
>
> 2016-06-16 15:05 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 6/16/16 6:10 AM, Luca Banetta wrote:
> >
> >> Dear gmx users,
> >> I am meeting a lot of problems launching a simulation with shell
> >> particles.
> >> The mdp file is
> >> ; VARIOUS PREPROCESSING OPTIONS
> >> title = Yo
> >> cpp = /usr/bin/cpp
> >> include =
> >> define =
> >>
> >> ; RUN CONTROL PARAMETERS
> >> integrator = md
> >> ; Start time and timestep in ps
> >> tinit = 0
> >> dt = 0.001
> >> nsteps = 1000000
> >> ; For exact run continuation or redoing part of a run
> >> init_step = 0
> >> ; mode for center of mass motion removal
> >> comm-mode = Linear
> >> ; number of steps for center of mass motion removal
> >> nstcomm = 1
> >> ; group(s) for center of mass motion removal
> >> comm-grps =
> >>
> >> ; LANGEVIN DYNAMICS OPTIONS
> >> ; Temperature, friction coefficient (amu/ps) and random seed
> >> bd-temp = 300
> >> bd-fric = 0
> >> ld-seed = 1993
> >>
> >> ; ENERGY MINIMIZATION OPTIONS
> >> ; Force tolerance and initial step-size
> >> emtol = 100
> >> emstep = 0.01
> >> ; Max number of iterations in relax_shells
> >> niter = 20
> >> ; Step size (1/ps^2) for minimization of flexible constraints
> >> fcstep = 0
> >> ; Frequency of steepest descents steps when doing CG
> >> nstcgsteep = 1000
> >> nbfgscorr = 10
> >>
> >> ; OUTPUT CONTROL OPTIONS
> >> ; Output frequency for coords (x), velocities (v) and forces (f)
> >> nstxout =
> >> nstvout =
> >> nstfout =
> >> ; Checkpointing helps you continue after crashes
> >> nstcheckpoint = 1000
> >> ; Output frequency for energies to log file and energy file
> >> nstlog = 50
> >> nstenergy = 50
> >> ; Output frequency and precision for xtc file
> >> nstxtcout = 50
> >> xtc-precision = 1000
> >> ; This selects the subset of atoms for the xtc file. You can
> >> ; select multiple groups. By default all atoms will be written.
> >> xtc-grps =
> >> ; Selection of energy groups
> >> energygrps =
> >>
> >> ; NEIGHBORSEARCHING PARAMETERS
> >> ; nblist update frequency
> >> nstlist = 5
> >> ; ns algorithm (simple or grid)
> >> ns_type = grid
> >> ; Periodic boundary conditions: xyz (default), no (vacuum)
> >> ; or full (infinite systems only)
> >> pbc = xyz
> >> ; nblist cut-off
> >> rlist = 0.9
> >> domain-decomposition = no
> >>
> >> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> ; Method for doing electrostatics
> >> coulombtype = Cut-off
> >> rcoulomb-switch = 0
> >> rcoulomb = 0.9
> >> ; Dielectric constant (DC) for cut-off or DC of reaction field
> >> epsilon-r = 1
> >> ; Method for doing Van der Waals
> >> vdw-type = Cut-off
> >> ; cut-off lengths
> >> rvdw-switch = 0
> >> rvdw = 0.9
> >> ; Apply long range dispersion corrections for Energy and Pressure
> >> DispCorr = EnerPres
> >> ; Extension of the potential lookup tables beyond the cut-off
> >> table-extension = 1
> >> ; Spacing for the PME/PPPM FFT grid
> >> fourierspacing = 0.12
> >> ; FFT grid size, when a value is 0 fourierspacing will be used
> >> fourier_nx = 0
> >> fourier_ny = 0
> >> fourier_nz = 0
> >> ; EWALD/PME/PPPM parameters
> >> pme_order = 4
> >> ewald_rtol = 1e-05
> >> ewald_geometry = 3d
> >> epsilon_surface = 0
> >> optimize_fft = no
> >>
> >> ; GENERALIZED BORN ELECTROSTATICS
> >> ; Algorithm for calculating Born radii
> >> gb_algorithm = Still
> >> ; Frequency of calculating the Born radii inside rlist
> >> nstgbradii = 1
> >> ; Cutoff for Born radii calculation; the contribution from atoms
> >> ; between rlist and rgbradii is updated every nstlist steps
> >> rgbradii = 2
> >> ; Salt concentration in M for Generalized Born models
> >> gb_saltconc = 0
> >>
> >> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> >> implicit_solvent = No
> >>
> >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> >> ; Temperature coupling
> >> Tcoupl = berendsen
> >> ; Groups to couple separately
> >> tc-grps = System
> >> ; Time constant (ps) and reference temperature (K)
> >> tau_t = 0.1
> >> ref_t = 300
> >> ; Pressure coupling
> >> Pcoupl = berendsen
> >> Pcoupltype = isotropic
> >> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >> tau_p = 1.0
> >> compressibility = 4.5e-5
> >> ref_p = 1.0
> >> ; Random seed for Andersen thermostat
> >> andersen_seed = 815131
> >>
> >> ; SIMULATED ANNEALING
> >> ; Type of annealing for each temperature group (no/single/periodic)
> >> annealing = no
> >> ; Number of time points to use for specifying annealing in each group
> >> annealing_npoints =
> >> ; List of times at the annealing points for each group
> >> annealing_time =
> >> ; Temp. at each annealing point, for each group.
> >> annealing_temp =
> >>
> >> ; GENERATE VELOCITIES FOR STARTUP RUN
> >> gen_vel = yes
> >> gen_temp = 300
> >> gen_seed = 1993
> >>
> >> ; OPTIONS FOR BONDS
> >> constraints = all-bonds
> >> ; Type of constraint algorithm
> >> constraint-algorithm = Lincs
> >> ; Do not constrain the start configuration
> >> unconstrained-start = no
> >> ; Use successive overrelaxation to reduce the number of shake iterations
> >> Shake-SOR = no
> >> ; Relative tolerance of shake
> >> shake-tol = 1e-04
> >> ; Highest order in the expansion of the constraint coupling matrix
> >> lincs-order = 4
> >> ; Number of iterations in the final step of LINCS. 1 is fine for
> >> ; normal simulations, but use 2 to conserve energy in NVE runs.
> >> ; For energy minimization with constraints it should be 4 to 8.
> >> lincs-iter = 1
> >> ; Lincs will write a warning to the stderr if in one step a bond
> >> ; rotates over more degrees than
> >> lincs-warnangle = 30
> >> ; Convert harmonic bonds to morse potentials
> >> morse = no
> >>
> >> ; ENERGY GROUP EXCLUSIONS
> >> ; Pairs of energy groups for which all non-bonded interactions are
> >> excluded
> >> energygrp_excl =
> >>
> >> ; NMR refinement stuff
> >> ; Distance restraints type: No, Simple or Ensemble
> >> disre = No
> >> ; Force weighting of pairs in one distance restraint: Conservative or
> >> Equal
> >> disre-weighting = Conservative
> >> ; Use sqrt of the time averaged times the instantaneous violation
> >> disre-mixed = no
> >> disre-fc = 1000
> >> disre-tau = 0
> >> ; Output frequency for pair distances to energy file
> >> nstdisreout = 100
> >> ; Orientation restraints: No or Yes
> >> orire = no
> >> ; Orientation restraints force constant and tau for time averaging
> >> orire-fc = 0
> >> orire-tau = 0
> >> orire-fitgrp =
> >> ; Output frequency for trace(SD) to energy file
> >> nstorireout = 100
> >> ; Dihedral angle restraints: No, Simple or Ensemble
> >> dihre = No
> >> dihre-fc = 1000
> >> dihre-tau = 0
> >> ; Output frequency for dihedral values to energy file
> >> nstdihreout = 100
> >>
> >> ; Free energy control stuff
> >> free-energy = no
> >> init-lambda = 0
> >> delta-lambda = 0
> >> sc-alpha = 0
> >> sc-sigma = 0.3
> >>
> >> ; Non-equilibrium MD stuff
> >> acc-grps =
> >> accelerate =
> >> freezegrps =
> >> freezedim =
> >> cos-acceleration = 0
> >>
> >> ; Electric fields
> >> ; Format is number of terms (int) and for all terms an amplitude (real)
> >> ; and a phase angle (real)
> >> E-x =
> >> E-xt =
> >> E-y =
> >> E-yt =
> >> E-z =
> >> E-zt =
> >>
> >> ; User defined thingies
> >> user1-grps =
> >> user2-grps =
> >> userint1 = 0
> >> userint2 = 0
> >> userint3 = 0
> >> userint4 = 0
> >> userreal1 = 0
> >> userreal2 = 0
> >> userreal3 = 0
> >> userreal4 = 0
> >>
> >>
> >> In the log file it is written that RMS force on the shell is -nan and
> it
> >> can't do EM.
> >> Can someone give me some advice in order to make EM possible?
> >>
> >
> > Please provide full details about what the system is and how you built
> > it. Also note that using plain cutoff electrostatics went out of style
> > about 20 years ago as it is horribly inaccurate.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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